The deadline to sign draft picks has passed and Mark Appel has decided to return to Stanford for his senior year instead of signing with the Pirates.

According to Jon Heyman, Appel declined the Pirates’ offer of $3.8 million and will take his chances again next season.

It would have been great to sign Appel, but this is not the end of the world. The Pirates will be compensated with the #9 overall pick in next season’s draft for failing to sign him, along with their pick they would normally get.

“We were unable to reach an agreement with first round selection Mark Appel and bring him into our already strong organization.

“Our final offer exceeded the available bonus pool money and was essentially up to the last dollar we could offer prior to falling into the second tier penalty which would have resulted in the loss of a first round draft selection. While, as we have shown in past years, we are willing to be aggressive with our financial offer, we simply did not feel it was in the best interest of the organization to forfeit our first round selection in the 2013 amateur draft.”

“Selecting Mark was a calculated risk, as we knew he would be a difficult sign. As an organization, we need to continue to take these types of calculated risks. While we would’ve preferred to add Mark to the group of talented prospects in our system, we wish Mark, and his family, nothing but success in the future.”

“We were able to add quality talent and depth from this year’s draft. We look forward to having the ninth selection in the 2013 draft as compensation for the non-signing of Mark, in addition to our conventional pick in the first round and beyond,to continue to further strengthen the talent level within our system.”

Based on that, it is apparent the Pirates were willing to pay the tax for going over their pool, but were not willing to give up draft picks, which is a wise move.

“After much thought, prayer, and analysis of both opportunities, I came to the conclusion the best decision is to remain at Stanford continuing my studies, finishing my degree, and doing all I can to assist the Cardinal baseball team in our goal to win a National Championship.

I greatly valued the prospect of a professional opportunity and I will pursue a professional baseball career after getting my Stanford degree.

I appreciate the love, support, and guidance from everyone who helped me make this decision.”

It looks like the Pirates are the first victims of Major League Baseball’s new draft rules, though. In the past, the Pirates outspent every other team to acquire as much talent as they possibly could. They were unable to that this season and were the only team that was unable to sign their first round pick because of it.